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vpc-ccg / pamir

Discovery and Genotyping of Novel Sequence Insertions in Many Sequenced Individuals
BSD 3-Clause "New" or "Revised" License
8 stars 4 forks source link

Investigate Specific Sites Only #4

Closed charliecurnin closed 6 years ago

charliecurnin commented 6 years ago

Hi guys,

Pamir looks like an awesome tool, and I'd love to try it. I have a sample, though, in which I've already identified a handful of specific insertions that I'd like to investigate—mostly find out what sequence was actually inserted there.

Is there a way I can run Pamir without having it process the entire genome? Can I somehow specify a bed file telling it to look just in certain regions? Alternatively, I know I can use samtools view to cut out specific regions from a BAM, but would this eliminate the orphan reads? It'd be great if there were a way to do this from FASTQ files too.

Thanks!

charliecurnin commented 6 years ago

I think I can do -m look_here.bed --invert-masker.